Contigs are contiguous fragments of DNA sequence from an incomplete draft genome.

Chimeric contigs are contigs that combine sequences from more than one genome. Short sequence reads from two different genomes can be incorrectly assembled into one contig due to a short region of similar sequence. Chimeric sequences are usually more frequent in 16S amplicon sequencing than in full genome shotgun sequencing.


Chimeric 16S sequences are merged rRNA seqments from different (but usually closely related) bacteria.

How to identify chimeric 16S sequences?

Chimeric sequences can be identified by testing whether the same sequence can be reconstructed by merging left and right-parts of two different 16S sequences, which are of higher presence/abundance in the same sample [DADA2].

see also:

→ DADA2 pipeline

→ usearch / uchime2 tools